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Plot

While sleeping near the Grand Canyon, a mosquito-like drone begins absorbing DNA from Ben's OMnitrix. Ben wakes up to see a large object crashing into the Grand Canyon, and Drones are rampaging in the Grand Canyon. Strangely, Ben can only change into Four Arms and Heatblast. After fighting most of the robots, Ben fights a giant robot, and after defeating it, it expels a crystal (referred to as Omnitrix Crystals); and by absorbing it into the Omnitrix, he is now able to change into XLR8.

The Tennysons see that Vilgax's drones and the Forever Knights are fighting each other. After fighting the Forever Knights at the Mesa Verde, one of them tells the Tennysons that Enoch is using technology from Area 51 to stop a dangerous threat. At Area 51, Ben fights Enoch, but he escapes with a giant robot made in his own image, using technology from the base. The Tennysons track Enoch to the Hoover Dam and fight him and his robot. After defeating Enoch, his robot expels another crystal and Ben regains Cannonbolt from it.

While heading to San Francisco for a real vacation, Kevin 11 shows up from a Null Void portal on the Golden Gate Bridge, and begins going on a rampage with Ben tracking him down. But Kevin brought some plant-like aliens with him (apparently from Wildvine's home world) and they begin joining the rampage as well. Kevin 11 kidnaps Grandpa Max, and Ben and Gwen track him to a lumber mill. After defeating him, Kevin is sucked back into the Null Void. Meanwhile, the Tennysons now focus on fighting the plant monsters Kevin brought back with him, tracking them to the top of the Seattle Space Needle. After beating the mother plant, Snap Dragon, it expels a third crystal and Ben regains Wildvine. Grandpa Max begins putting together clues taken from the past battles and realizes that Vilgax is behind it all.

It is revealed that Ghostfreak has freed Vilgax from the Null Void and has teamed up with him to get revenge on Ben. While camping at the Effigy Mounds, Ben, Gwen, and Max are attacked by Zs'Skayr's minions. While fighting them, they encounter Hex, who plans on taking over the Earth by opening a portal from Earth to Anur Phaetos, Zs'Skayr's home dimension, (the source of the minions) to create an army. After beating Hex, it is revealed that he was actually possessed by Zs'Skayr. At the Plumber base of Mount Rushmore, Zs'Skayr steals the Ethereal Amplifier for Vilgax. Ben tracks Zs'Skayr to the Chicago Lake Front, where the latter reveals that he has used the crystals to supercharge three of his minions to fight Ben. After defeating Zs'Skayr at the Gold Coast Theater, Grandpa Max sends Zs'Skayr to the Null Void. After the battle, Gwen finds another crystal; it doesn't unlock any aliens, but it does give Ben almost full power in the Omnitrix.

Ben tracks the rest of his alien DNA to a re-enactment of the Civil War at New Orleans, and while searching, the Tennysons are attacked by Dr. Animo's mutants. To make matters worse, Animo kidnaps Gwen. After tracking and defeating Clancy at a bayou, they learn from him that Animo is planning on turning Gwen into a mutant, along with the rest of the world. Tracking Animo to an abandoned oil refinery, where it is secluded and has sufficient power for his machines, Ben fights and defeats him, saving Gwen. They learn from Gwen that Animo partnered with Vilgax as well, and is planning to send the entire Earth into the Null Void using the stolen Plumber Technology that is powered by alien DNA. After beating Animo, Ben gets the Master Control of the Omnitrix.

The Tennysons go to Washington D.C. to warn the government of Vilgax's plan; meanwhile, Null Void portals are opening everywhere. However, the government cannot respond, so the Tennysons go to Cape Canaveral to get to Vilgax's ship via strapping rockets on to the Rust Bucket, making it space worthy. After defeating Sixsxi, Ben goes to fight Vilgax, while Gwen and Max focus on trying to stop Vilgax's plan. Vilgax is defeated and sent into the Null Void along with his ship, but not before the Tennysons can escape and take back the rest of Ben's alien DNA.

As Vilgax is repaired by his nanobots in the Null Void, he swears that he will return someday. The last area is the Null Void where Ben fights all of his enemies again. In the final scene, Gwen tells Ben how impressed she is, while Grandpa Max looks for a way out of the Null Void.